Quick viewing(Text Mode)

Operational Guidelines for Intensified National Sari Surveillance

Operational Guidelines for Intensified National Sari Surveillance

OPERATIONAL GUIDELINES FOR INTENSIFIED NATIONAL SARI SURVEILLANCE

IHR, Alert and Response, and Project Pan American Health Organization Washington, D. C. January 2011 CONTENTS

Introduction______3

1. Overview ______5

1.1. Background ______5

1.2. The International Health Regulations ______5

1.3. The Epidemiology of ______6

1.4. Clinical Description of Influenza______10

1.5. Influenza and SARI surveillance ______11

1.6. Influenza Surveillance ______13

2. Intensified National Surveillance of SARI______15

2.1. Introduction ______15

2.2. Specific surveillance objectives______15

2.3. Purpose of surveillance______16

2.4. Type of surveillance ______16

2.5. Area of surveillance______16

2.6. Target population for surveillance ______16

2.7. Seasonality ______16

2.8. Data management______16

2.8.1. Data Collection Forms ______17

2.8.2. Data collection steps ______17

2.8.3. Data Analysis ______20

2.9. Organizing the Intensified National Surveillance System ______29

2.10. Information Flow ______31

Bibliography ______32

ANNEX I - Collecting, Storing and Transporting Specimens of Respiratory Secretions for Identification ______37

October 2010 version 1

ANNEX II – Process Evaluation and Analysis of Surveillance Data ______51

ANNEX III – Control ______56

ANNEX IV – Data Collection Forms ______62

ANNEX V – INFLU Data Analysis Application ______Error! Bookmark not defined.

October 2010 version 2

Introduction Emerging respiratory infectious diseases pose a substantial risk for humans due to their extremely high potential to spread from person-to-person. These diseases can produce high morbidity and mortality.

There have been several incidents of emerging respiratory infectious diseases in the last hundred years, including the influenza of 1918 known as the “”, the 1957 “Asian flu” pandemic, the 1968 “” pandemic, the 2003 Severe Respiratory Syndrome (SARS) pandemic, and the influenza A (H1N1) pandemic of April 2009. All of these events demonstrate the importance of having a respiratory surveillance system that can detect new rapidly and provide information to assess impact on the population and having operational preparedness plans.

The International Health Regulations [IHR (2005)] in effect since 15 June 2007 require all Member States to strengthen their surveillance and response capacities for events with major public health implications. Under the IHR (2005), PAHO/WHO is to be notified immediately of all cases of the following diseases: , poliomyelitis (due to wild ), SARS, and human influenza due to new virus subtypes.

To strengthen basic surveillance and response capacities and integrate the epidemiological surveillance of influenza with laboratory surveillance into one system, the Pan American Health Organization (PAHO), in collaboration with the Centers for Disease Prevention and Control (CDC), developed a Generic Protocol for Influenza Surveillance, along with two operational guides designed primarily for local health teams in the PAHO Member States. The first operational guide was designed to help prepare facilities for unusual or unexpected cases or clusters of severe acute respiratory infection (SARI), while the second was designed to systematize approaches to the implementation of sentinel surveillance of influenza-like illness (ILI) and SARI.

One important lesson learned from the 2009 was the importance of obtaining information about severe cases. To that end, resources should be focused on expanding SARI surveillance.

The purpose of this document is to provide a tool to support countries in implementing intensified SARI surveillance. October 2010 version 3

October 2010 version 4

1. Overview 1.1. Background

On 24 April 2009, the World Health Organization (WHO) notified Member States of human cases of A (H1N1) in Mexico and the United States. The following day, pursuant to the International Health Regulations (IHR-2005) the event was declared to be a public health emergency of international importance. On 11 June 2009, a WHO statement declared phase six of preparations for the pandemic to be implemented worldwide. In other words, human infection caused by the 2009 pandemic influenza virus A (H1N1) 2009 had spread at the community level on more than two continents. As of 10 August, 2010, when the pandemic was declared over by WHO, more than 213 countries, representing all the continents, had reported confirmed cases of infection caused by the new virus, including 18,449 deaths, 8,557 of which were in the Region of the Americas.

1.2. The International Health Regulations

The International Health Regulations (IHR) are a set of binding legal instruments adopted by the Member States of the World Health Organization (WHO) to contain the spread of disease.

The most recent revision of the regulations (2005) is an updated version of the 1969 regulations, which specified only four notifiable diseases – , plague, yellow and smallpox (now eradicated). The 1969 version set forth general border control provisions, as well as relatively passive notification and monitoring measures. The new version – an unprecedented international public health agreement – provides for containing health emergencies at their local points of origin, rather than limiting action to national borders.

The IHR (2005) have been in effect since 15 June 2007. It covers all diseases and health events that can have serious public health impact and that have the potential for international propogation. These diseases can range from emerging such as SARS and new human influenza viruses to chemical spills or leaks and nuclear accidents. The IHR specify a series of procedures for the management of such events, as well as basic requirements for national surveillance and response. These core competencies include the capacities to detect, investigate, confirm, notify, and take action on diseases or health events that could constitute public health emergencies of international significance.

October 2010 version 5

Under the IHR (2005), PAHO/WHO should be notified immediately of all cases of the following diseases: smallpox, poliomyelitis (due to wild poliovirus), SARS, and human influenza caused by new virus subtypes. Annex II of the IHR (2005) refers to the surveillance, exchange of information, consultation, confirmation, and public health response to any new influenza virus subtype with pandemic potential. These notifications are to include assessments of human risk from occurring in avian populations. Detecting such outbreaks is responsibility of the World Organization for Animal Health (OIE).

1.3. The Epidemiology of Influenza

The influenza virus The influenza virus is an RNA virus of the orthomomyxoviridae family. There are three types of the virus capable of causing disease in humans which have been identified—A, B, and C. However, only the A viruses, which are highly mutatable, have caused . The B viruses have caused sporadic outbreaks with high mortality in older adults, while the C viruses are usually associated with mild disease.

Subtypes of the influenza A viruses also have designations, which are based on the and proteins present on their surface (Figure 1). Sixteen hemagglutinin subtypes and nine neuramidase subtypes have been identified.

At present, the subtypes pandemic (H1N1) 2009 and H3N2 in circulation are responsible for seasonal (Table 1). The H5, H7 and H9 viruses rarely produce disease in humans.

Figure 1 Characteristics of the influenza A virus

October 2010 version 6

Lipoprotein shell with glycoprotein surface projections in the form of: • Hemagglutinin (H) 16 • Neuraminidase (N) 9 antigens

Table 1 Influenza A viruses responsible for the last four pandemics Virus type/subtype Pandemic Year A/H1N1 Spanish Flu 1918 A/H2N2 Asian Flu 1957 A/H3N2 Hong Kong Flu 1968 A/H1N1 Influenza H1N1 2009

Influenza A viruses have two principal features that give them major pandemic potential: • antigenic variability • an extensive animal reservoir, especially wild aquatic birds, which are a natural reservoir of all the known influenza subtypes

The phenomenon of influenza A epidemics and pandemics is due to the frequency with which the genetic composition of influenza A viruses changes.

Genetic changes, known as “”, cause minor alterations of the antigens on the viral surface of the influenza virus. Drift is a continuous process that produces new antigenic variants and hence necessitates annual modification of influenza composition.

October 2010 version 7

The larger genetic changes known as “antigenic shifts” are more radical, involving the appearance of viruses with new or new combinations of hemagglutinin and neuraminidase. There are two main mechanisms of : (a) , which involves an exchange of genetic material between an influenza virus of nonhuman origin and one of human origin when both are present in a human being or intermediate mammal such as a , and (b) a more gradual process of adaptive through replication in successive human infections, which gives the virus an increasing ability to unite with human cells and transform itself into a new virus with full capacity to circulate in humans.

Reservoirs

The influenza A virus is found in numerous animal species. However, its principal reservoir is wild aquatic birds, which can transmit the infection to other birds, both wild and domestic, and to various mammals, including humans, whales, , horses, and domestic and wild felines. The pig has been considered an intermediate reservoir serving as a mixing vessel for exchange of genetic material between different influenza viruses.

Transmission

The influenza virus is transmitted in the following ways: • Direct contact: o from person to person at a distance of less than one meter o through droplets of over 5 μm that generally travel up to one meter and are generated when an infected individual or o through generating procedures (droplet nuclei of up to 5 μm that travel over one meter) • Indirect contact: o through contaminated objects ()

The virus can survive outside a living organism—five minutes on the hands, 8-12 hours on paper, cloth, and other fibers, and 24-48 hours on hard surfaces.

October 2010 version 8

The contagious period ranges from one day before the onset of symptoms to 3-7 days after. Even if a person is , he/she can transmit the virus. Children and people with immunodeficiencies may shed the virus over longer periods of time.

The influenza virus has high attack rates and spreads rapidly in closed environments. Attack rates in non-pandemic years can reach 30% in schoolchildren and between 1% and 15% among adults. Attack rates in institutional settings can be even higher.

The transmission of pandemic influenza virus H1N1 is similar to that of the seasonal variety. Figure 2, below, shows case rates, hospitalization rates, and mortality. These are estimates based on the first wave of the H1N1 2009 pandemic.

Figure 2 Estimated attack rate, percent hospitalized, and percent mortality for the pandemic virus H1N1 2009

Source: Weekly Epidemiological Record No. 49, 2009, 84, 505-516. Available at: http://www.who.int/wer

October 2010 version 9

1.4. Clinical Description of Influenza

The for the virus ranges from 1 to 4 days, and averages 2 days. The disease’s manifestations vary widely. The infection may be asymptomatic, may produce an influenza syndrome, or may develop into an illness serious enough to cause death. The symptoms span a broad clinical spectrum, including fever of ≥38oC, , sore , , , , prostration, and coryza, as well as gastrointestinal symptoms. The cough can be intense and of longer duration, but the other symptoms are shorter-term, and patients recover in two to seven days. Clinically, influenza is not always distinguishable from diseases caused by other respiratory viruses.

Symptoms vary according to the patient’s age, underlying comorbidities, and individual immune response. In children, the clinical presentation includes high fever, cervical , and , and gastrointestinal symptoms. Although young children are unable to describe their symptoms, the presence of a is detectable because they cry when eating, find it difficult to eat, salivate, vomit, or have vocal changes. Older adults almost always present with fever, though not as high as that observed in children, but sometimes without any other symptoms.

Serious complications and death occur mainly in the elderly, in children, in institutionalized individuals, and in persons with chronic disease or (e.g. heart disease, hemoglobinopathies, metabolic disease, pulmonary and renal diseases, and AIDS). Pregnant women have been shown to have increased morbidity and mortality associated with influenza infection.

While the influenza virus can cause a primary infection of the upper and/or lower , rarely, it can occur with another virus or bacteria, a situation known as a co-infection. Bacterial co-infections are often secondary infections that result from the initial viral changes caused by the influenza virus in the respiratory tract, which facilitate the invasion by bacteria. Secondary bacterial co-infections are most often due to pneumoniae, or .

Annual deaths from influenza worldwide are estimated to be as high as one million.

October 2010 version 10

1.5. Influenza and SARI surveillance

Given that influenza does not cause a specific clinical syndrome that differentiates it from other (Table 2), it is not possible to identify patients with influenza without a diagnostic test. This is complicated, however, by the fact that it is not practical, from the standpoint of resource utilization, to test all suspect patients for influenza. For these reasons, a proxy respiratory syndrome is used, which is felt to be sensitive to detect influenza cases, and a subset of these patients is tested for influenza.

Table 2 Principal viruses responsible for Acute Respiratory Infections Syndromes Etiologic agents Clinical manifestations Influenza-like Illness Influenza, Adenovirus, Fever (38oC), sore throat, , Parainfluenza, cough. May be , Respiratory accompanied by , Syncytial Virus (RSV) myalgia, headache, nasal congestion. Adenovirus, Coronavirus, Headache, nasal () Influenza, Parainfluenza, congestion Rhinovirus, Respiratory malaise, myalgia. Syncytial Virus (RSV) Coronavirus, Influenza Localized oropharyngeal Rhinovirus, Respiratory . Syncytial Virus (RSV) Laryngotracheobronchitis Adenovirus, Influenza, Fever, dry and persistent () Parainfluenza, Respiratory cough, hoarseness. Syncytial Virus (RSV) Bronchiolitis Influenza, Respiratory Dry and persistent cough, Syncytial Virus tachypnea, wheezing observed through pulmonary auscultation, and chest X-ray alterations. Adenovirus, Influenza, Systemic symptoms such Hantavirus, Parainfluenza, as fever, malaise, and dry

October 2010 version 11

Measles, Varicella, cough in association with Respiratory Syncytial Virus tachypnea and alterations (RSV) observed through pulmonary auscultation or chest X-ray. Source: Adapted from the “Plano de Preparação Brasileiro para o enfrentamento de uma pandemia de influenza”, Série B, Textos Básicos em Saúde, Secretariat of Health Surveillance, Ministry of Health of Brazil, Brasília, D. F., 2005.

Given that a proxy syndrome is used, one reality is that not all captured patients will have influenza. As mentioned, above, there are many other pathogens that cause respiratory illness similar to influenza (Figure 3) and for this reason, it is important to monitor the percent of the syndromic cases that are positive for influenza as well as other pathogens.

Figure 3 Etiologic agents of severe acute respiratory infections

October 2010 version 12

1.6. Influenza Surveillance

Surveillance is essential to monitor events that might jeopardize the health of a population so that appropriate prevention and control measures can be implemented in a timely manner.

The following are criteria that can be used to decide which events to survey: 1. Utilize the IHR (2005) criteria, relating to smallpox, poliomyelitis (due to wild poliovirus), SARS, human influenza caused by new viral subtypes, and other public health events of international significance 2. Monitor the events that are most relevant to the country’s public health because of their magnitude, potential for spread and impact based on the population’s vulnerability 3. Utilize the goals set in conjunction with other international partners such as those that the countries of the Americas have made to PAHO/WHO for the eradication/elimination of , , and congenital rubella syndrome, and introduction influenza (Resolution 10 of the 47th Directing Council of the PAHO Member Countries, September 2006).

The following are the objectives of influenza surveillance, as set forth in the PAHO/CDC Generic Protocol:

• Detect the appearance of new influenza subtypes on a timely basis, as called for by the IHR (2005)

• Detect unusual or unexpected outbreaks of viral respiratory diseases

October 2010 version 13

• Identify the epidemiological characteristics of influenza and other viral respiratory diseases (such as those caused by Adenovirus, Parainfluenza and respiratory syncytial virus) • Monitor influenza viruses to help formulate recommendations for the annual composition of and to determine the vaccine concordance with circulating influenza strains • Provide data to calculate the ILI and SARI burden in humans • Provide data to guide and control measures • Assess impact of implemented prevention and control measures In order to achieve these objectives, the Generic Protocol recommends conducting two types of influenza surveillance (Figure 4):

• Sentinel surveillance of: o ILI in the outpatient setting o SARI in hospitals and health facilities that provide inpatient treatment • Intensified national surveillance to detect unusual or unexpected cases of severe acute respiratory infection, which all health facilities should be equipped to detect

Figure 4 Types of influenza surveillance (PAHO/CDC Generic Protocol)

During the pandemic of 2009, in the Americas Region, limited data were available to make decisions about disease severity. So, one important lesson learned was the need to strengthen and enhance surveillance of severe cases.

October 2010 version 14

2. Intensified National Surveillance of Severe Acute Respiratory Infection (SARI)

SARI: case definition

• sudden onset of fever >38oC AND • cough or sore throat AND • difficulty breathing (dyspnea) AND • need for hospitalization

Respiratory rate is a very useful parameter in evaluating dyspnea or difficulty breathing (Table 1). Another parameter which can be used to evaluate difficulty breathing is oxygen saturation while breathing ambient air. Measured by digital , saturation should be 95% or greater. Saturation < 90% is an indication of severe disease, while in pregnant women, <95% can indicate severe disease. Table 1 Upper limits of respiratory rate by age AGE Increased respiratory rate (tachypnea) < 2 months > 60 breaths/minute 2-11 months > 50 breaths/minute 12 months to 5 years > 40 breaths/minute Adults > 26 breaths/minute

2.1. Introduction

Acute respiratory infections, including influenza-type illnesses (ILIs), are typically managed in the outpatient setting. However, when serious symptoms and signs develop, patients should be hospitalized. It is these hospitalized patients that are eligible for inclusion in the SARI surveillance system.

2.2. Specific surveillance objectives

• Determine the proportion of hospitalizations, ICU admissions, and deaths associated with SARI

• Determine the relative burden of respiratory viruses causing SARI

October 2010 version 15

• Determine the seasonal patterns of respiratory virus circulation

• Determine the types/subtypes of circulating influenza viruses

• Describe the epidemiology of influenza

• Detect early the emergence of novel and high pathogenicity influenza viruses

• Provide viruses for the development of seasonal and pandemic influenza vaccines

• Provide data to estimate the disease burden of influenza

2.3. Purpose of surveillance

• To provide information to make decisions about the prevention and control of influenza

2.4. Type of surveillance

• Hospital-based surveillance

2.5. Area of surveillance

• Nationwide

2.6. Target population for surveillance

• Individuals of all ages and both sexes

2.7. Seasonality

• Year-round, as tropical climates do not have well-defined influenza seasons and a novel influenza subtype can emerge anytime

2.8. Data management

Epidemiologic component: To determine the epidemiological characteristics of SARI cases, data should be collected on all cases admitted to the hospital. These data should include the number of hospitalized SARI

October 2010 version 16 cases, the number of SARI cases admitted to ICUs, and the number of SARI. All data should be stratified by sex, age, risk factors, and presence/absence of a sample.

Additionally, the total number of all-cause hospitalizations, ICU admissions, and deaths should be collected and used as the denominator, to calculate a proportion. Sites which are able to estimate the catchment area should use it as the denominator to calculate incidence.

Etiologic component: To determine the etiology of the SARI cases, respiratory specimens should be collected from all patients meeting the SARI case definition.

Note: specimens should be collected throughout the year, regardless of the season

2.8.1. Data Collection Forms

The forms provided in Annex IV are recommended for recording the data • Form IÍI – Consolidated daily or weekly data on all-cause hospitalizations, ICU admissions, and deaths and all SARI hospitalizations, ICU admissions, and deaths.

2.8.2. Data collection steps

All patients meeting the SARI case definition should be counted, even if a specimen cannot be collected

Case Identification and Collection of Epidemiologic Information 1. Select those hospitalized patients that meet the case definition of SARI. -To identify potential SARI cases and deaths, the 10th revision of the International Classification of Diseases (ICD 10) is recommended as a reference. Upper respiratory infections (ARIs) are classified from J00 to J06 (Table 2), and lower respiratory infections from J09 to J18 and from J20 to J22 (Table 3). However, care should always be taken to note whether the case identified from the ICD-10 codes, meets the SARI case definition—for example, ensuring that a hospitalized patient with bronchitis, in addition to cough and dyspnea, has fever. If ICD-10 codes are not available until discharge, the codes can be used as a quality control measure to confirm that all potential cases are being identified. October 2010 version 17

Table 2 – ICD 10, upper ARI ICD-10, upper ARI Description J00 Flu or common cold J01 Acute

J02 Acute pharyngitis

J03 Acute

J04 Acute and

J05 Acute obstructive laryngitis and

J06 Upper respiratory infections at multiple sites

Source: World Health Organization

Table 3 – ICD 10, lower ARI

ICD-10, lower ARI Description J09 Influenza due to avian virus J10 Influenza due to another identified virus J10.0 Influenza with , identified viruses J10.1 Influenza with other respiratory J10.8 manifestations, identified viruses Influenza with other manifestations, identified viruses J11 Influenza due to unidentified virus J11.0 Influenza with pneumonia, identified virus J11.1 Influenza with other respiratory J11.8 manifestations, unidentified virus Influenza with other manifestations, unidentified virus

October 2010 version 18

J12 not classified elsewhere J12.0 Viral pneumonia due to adenovirus J12.1 Viral pneumonia due to RSV J12.2 Viral pneumonia due to parainfluenza J12.8 Viral pneumonia, other etiology J12.9 Viral pneumonia, unspecified J13 Pneumonia due to J14 Pneumonia due to Haemophilus influenzae J15 not classified elsewhere J16 Pneumonia due to another infectious agent, not classified elsewhere J17 Pneumonia in other diseases classified elsewhere (see ICD-10 specifications) J18 Pneumonia due to an unspecified agent J20 (see ICD-10 specifications) J21 Acute bronchiolitis J21.0 Acute bronchiolitis due to RSV J21.8 Acute bronchiolitis due to another infectious J21.9 agent Acute bronchiolitis due to an unspecified agent J22 Unspecified acute lower respiratory infection Source: World Health Organization 2. Complete Form III daily for every patient admitted with SARI (including hospitalized and ICU patients and deaths) Specimen Collection 3. Collect respiratory specimens from patients meeting the SARI case definition, preferably presenting within three days (72 hours) of onset of fever, but within 10 days at the most 4. Independent of time since onset of symptoms, sample: o every SARI patient admitted to ICU o every death admitted with SARI 5. Prepare materials for sample collection

October 2010 version 19

6. Collect sample with special attention to infection control principles and biosafety standards (Annex III), using appropriate PPE 7. Prepare specimens for storage and transportation (see Annex I) in accordance with biosafety standards and send to hospital laboratory

Figure 1 SARI surveillance steps

2.8.3. Data Analysis

There are three key steps to the data analysis procedure: compiling the data, assessing the quality of the data, and analyzing the data.

1. Data compilation Data should be compiled at least once a week. Data should be organized the in the following manner:

By sex and age group* a. Total number of hospitalizations b. Total number of hospitalizations for SARI c. Total number of ICU admissions

October 2010 version 20

d. Total number of ICU admissions for SARI e. Total number of deaths f. Total number of deaths associated with SARI g. Number of SARI hospitalized cases with underlying comorbidities h. Number of SARI ICU admissions with underlying comorbidities i. Number of SARI-associated deaths with underlying comorbidities j. Number of SARI hospitalized cases who received antiviral treatment k. Number of SARI ICU admissions who received antiviral treatment l. Number of SARI-associated deaths who received antiviral treatment m. Number of SARI hospitalized cases who received the current seasonal n. Number of SARI ICU admissions who received the current seasonal influenza vaccine o. Number of SARI-associated deaths who received the current seasonal influenza vaccine p. Number of SARI cases (hospitalizations, ICU admissions, and deaths) positive for influenza and other respiratory viruses q. Total number of samples collected and tested

Information about age should be collected in the following age categories and can be later aggregated if needed: • 0-5 months • 6-11 months • 12-23 months • 2-4 years • 5-9 years • 10-14 years • 15-19 years • 20-24 years • 25-29 years • 30-34 years • 35-39 years • 40-49 years • 50-59 years

October 2010 version 21

• 60-64 years • > 65 years

The rationale for using these age groups has to do with the following factors: • The vaccine is not used in infants under 6 months of age • is a universal indicator, and it is important to have data on the contribution of influenza to morbidity and mortality • Increased risk for morbidity and mortality has been shown in the age extremes

2. Data critique It is important to review the data on a routine basis to ensure that all quality standards are being met (Annex II). The general questions to be answered are: Are the data complete? Are they timely? Are they consistent?

3. Data analysis Below are the key indicators to calculate and the recommended outputs.

KEY INDICATORS a. Overall and by age:

• The proportion of hospital admissions for SARI

Calculation: Total number of admissions for SARI during the reporting period

Total number of medical admissions during the reporting period

• The proportion of ICU admissions for SARI

Calculation: Total number of ICU admissions for SARI during the reporting period

Total number of ICU medical admissions during the reporting period

• The proportion of deaths associated with SARI

Calculation: Total number of deaths associated with SARI during the reporting period

Total number of deaths during the reporting period b. For SARI hospitalized cases, SARI ICU cases, and SARI deaths:

October 2010 version 22

• The number of cases with underlying co-morbid conditions

• The number of cases who received the seasonal influenza vaccine

• The number of cases who received antiviral therapy c. Of all samples tested, the proportion of samples positive for influenza Calculation: Total number of influenza-positive samples during the reporting period

Total number of samples tested during the reporting period d. The distribution of influenza positive cases by type and subtype e. Of all samples tested, the proportion of samples positive for any respiratory virus Calculation: Total number of respiratory-positive samples during the reporting period

Total number of samples tested during the reporting period f. The distribution of respiratory virus positives cases g. Overall, by age group, and by case severity (i.e. SARI hospitalized cases, SARI ICU cases, and SARI death), the distribution of respiratory virus positive cases

OUTPUTS a) A line graph showing the proportion of hospitalizations, ICU admissions, and deaths associated with SARI. If the catchment area of the surveillance site is known, incidence instead of proportions can be calculated.

• Overall (i.e. for all age groups)

October 2010 version 23

SARI (%): hospitalizations, ICU admissions & deaths by EW, Country XXXX, 2011 20% 18% 16% 14% 12%

% 10% 8% 6% 4% 2% 0% 1 2 3 4 5 6 7 8 9 101112131415161718192021222324252627282930 EW % SARI % SARI admitted in ICU % SARI deaths

October 2010 version 24

• By age group (<5 years, 5-17 years, 18-49 years, 5-64 years, ≥65 years) SARI (%): hospitalizations, ICU admissions and deaths by EW, Country XXXX, 2011

< 5 years Under 5 years of age 20% 16%

12% % 8% 4% 0% 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 EW

5 ‐ 17 years 20% 5 - 17 years 16% 12% % 8%

4% 0% 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 EW

18 ‐ 49 years 20% 18 - 49 years 16%

12% % 8% 4%

0% 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 EW

50 ‐ 64 years 50 - 64 years 20% 16%

12% % 8%

4% 0% 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 EW

October 2010 version 25

≥ 65 years 20% ≥ 65 years 16%

12% % 8% 4% 0% 1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 EW

b) A table showing the proportion of cases in each severity category with underlying comorbidities, history of vaccination, and history of antiviral therapy. The data shown are fictitious.

SARI hospitalized (n=100) SARI ICU (n=100) SARI deaths (n=100)

n (%) n (%) n (%) Comorbid conditions 50 (50) 75 (75) 75 (75) • 5 (10) 10 (7.5) 10 (7.5) • Chronic Respiratory 5 (10) 10 (7.5) 10 (7.5) • Neurological 5 (10) 10 (7.5) 10 (7.5) • Immunosuppression 5 (10) 10 (7.5) 10 (7.5) • Chronic Renal 5 (10) 10 (7.5) 10 (7.5) • Cardiac Disease 5 (10) 10 (7.5) 10 (7.5) • 5 (10) 10 (7.5) 10 (7.5) • Obesity 5 (10) 5 (6.7) 5 (6.7) • Chronic Hepatic 10 (20) 0 0 • Pregnancy 10 (20) 5 (6.7) 5 (6.7) Seasonal influenza* 10 (10) 10 (10) 20 (20) vaccine therapy 10 (10) 10 (10) 20 (20) *Depending on the time of the year and the country, this will be either the Northern or Southern Hemisphere formulation

October 2010 version 26 c) A combined line graph and bar chart showing the distribution of influenza cases by type and subtype with the percent positivity for influenza. The example here is from the U.S. CDC.

d) A combined line graph and bar chart showing the distribution of all respiratory viruses with the percent positivity for any respiratory virus. These are data reported to PAHO by Mexcio.

Mexico Distribution of respiratory viruses under surveillance by EW 350 2010, as reported to PAHO 90

80 300 70 250 60

200 50

150 40

30 Positives %

Number of CasesNumber of 100 20 50 10

0 0 13579111315171921232527293133353739414345474951 Epidemiological Week

RSV Adenovirus Parainfluenza Flu A (not subtyped) Flu A Seasonal (H3) Flu H1N1 (pandemic) Flu B % Positives

October 2010 version 27 e) A bar graph showing the distribution of respiratory viruses by age group. The same age groups should be used as those for the SARI graph. The graph below, from Chile’s Ministry of Health, is an example.

f) A bar graph showing the distribution of respiratory viruses in each severity category. The data shown are fictitious.

October 2010 version 28

Distribution of Virus Types by SARI Case Severity- May 2011

100

80

60

40 Percent 20

0 Hospitalized (N=100) ICU (N=50) Deaths (N=25) Severity of Case

RSV Para Adeno Influenza A Influenza B

4. Interpret tables and figures

• Examine trends over time

• Assess which risk groups are being most affected

• Assess patterns to determine temporality

• Identify acute or unusual events which necessitate immediate follow-up

2.9. Organizing the Intensified National Surveillance System

National SARI surveillance should be integrated within the country’s epidemiological surveillance system. To that end, each country should determine the structure of the system that best utilizes and incorporates the country’s resources and realities. In general, there must be a team, the size of which each country will determine, at the surveillance site, within the laboratory, and at the ministry of health, who are dedicated to SARI surveillance. The following paragraphs delineate the general tasks to complete at each level.

Local-level surveillance site responsibilities • Identify cases meeting the SARI case definition • Select SARI cases for which specimens are to be collected • Collect respiratory specimens utilizing appropriate infection control practices, including PPE

October 2010 version 29

• Prepare specimens for shipment to the laboratory • Arrange for shipment of specimens to the laboratory under the appropriate biosafety conditions • Complete Forms I and II • Immediately notify the Ministry of Health of any unusual SARI cases • Enter and assess data on a daily basis • Conduct data analyses and prepare epidemiologic reports on a weekly basis • Report any situation outside normal parameters to the ministry of health

Laboratory responsibilities • Train personnel on proper technique for collecting, preparing, and transporting specimens • Confirm that biosafety standards for handling and transporting specimens are being followed • Process specimens on a timely basis • Complete Form III with the laboratory test results and the test date • Communicate results to the surveillance site and the ministry of health • Monitor positivity index to ascertain whether it is within the expected ranges • Indentify issues with sample collection, preparation, and transport that are affecting laboratory test results • Routinely send influenza viruses, according to the protocol, to the Centers for Disease Control (CDC) laboratory in Atlanta, USA • Send unsubtypeable influenza viruses to the Centers for Disease Control (CDC) laboratory in Atlanta, USA, immediately • Collaborate in data analysis and process evaluation • Collaborate in the preparation and dissemination of reports • Report virologic results to PAHO and WHO through the systems established for the purpose

National level (i.e. Ministry of Health) responsibilities • Coordinate the surveillance process, including providing the resources needed to sustain the surveillance program • Collaborate with the laboratory to conduct surveillance training and awareness activities • Monitor activities in each hospital to identify and resolve problems October 2010 version 30

• Promote integrated work between the laboratory and each hospital • Periodically evaluate the quality of the data being obtained • Prepare, in collaboration with the local surveillance team and laboratory personnel, the national report on a weekly basis • Disseminate the weekly report to all relevant stakeholders, including PAHO • Disseminate public health alerts regarding events of national and/or international importance

Within the hospital setting, hospitals should consider how SARI surveillance can be integrated into the other hospital surveillance systems, so as to create a sustainable program. One such approach is to create a department of hospital surveillance and epidemiology that deals both with community-acquired infections as well as health care-associated infections.

2.10. Information Flow

The information generated in each hospital in collaboration with the laboratory should be sent to the next highest hierarchical level, and from there to the next, until the national level is reached.

In order to provide feedback for the system, the information consolidated at the national and subnational levels should follow the same route back, through all the intermediate levels to the hospital and laboratory.

The national level will notify PAHO through the surveillance coordinator, using the information system provided by PAHO. PAHO will be responsible for disseminating the information in other world regions.

October 2010 version 31

Figure 2

Bibliography 1. Brazil. Ministry of Health. Secretariat of Health Surveillance. Plano de Preparação Brasileiro para o enfrentamento de uma pandemia de influenza, Série B, Textos Básicos em Saúde, Ministry of Health of Brazil, Brasília, D.F., 2005. [Accessed 25 February 2009]. Available at: http://dtr2001.saude.gov.br/influenza/docs/flu1.pdf 2. Cao B et al. Clinical Features of the Initial Cases of 2009 Pandemic Influenza A (H1N1) Virus Infection in . N Engl J Med 2009; 361. 3. Center for Disease Control and Prevention. Prevention and Control of Influenza. Recommendations of the Advisory Committee on Immunization Practices (ACIP) MMWR. 2006; 55 (No. RR-10). 4. Centers for Disease Control and Prevention. Prevention and Control of Influenza. Recommendations of the Advisory Committee on Immunization Practices (ACIP) 2008 MMWR. 2008; 57 (No. RR-7). 5. Centers for Disease Control and Prevention. Safety of Influenza A (H1N1) 2009 Monovalent Vaccines – United States, October 1 - November 24, 2009. MMWR Early Release Vol. 58/December 4, 2009.

October 2010 version 32

6. Centers for Disease Control and Prevention. [Homepage on the Internet]. Influenza Antiviral : A Summary for Clinicians. [Updated 17 July 2008, accessedAvailable at: http://www.cdc.gov/flu/PROFESSIONALS/ANTIVIRALS/SUMMARY-CLINICIANS.HTM. 7. Clark TW et al. Trial of 2009 Influenza A (H1N1) Monovalent MF59-Adjuvanted Vaccine. N Engl J Med 2009; 361:2424-35. 8. Cox NJ, Subbarao K. Influenza. Lancet 1999; 354:1277-82. 9. Heymann, DL. Control of communicable diseases. 18th edition, Scientific and Technical Publication No. 613, PAHO/WHO. Washington, D.C.. 2005. p: 379--380. 10. Food and Agriculture Organization (FAO), World Organization for Animal Health (OIE) in collaboration with World Health Organization (WHO). A Global Strategy for the Progressive Control of Highly Pathogenic (HPAI). October 2005 [accessed 25 February 2009]. Available at: http://un-influenza.org/files/aj134e00.pdf 11. World Health Organization. Guidelines on the Use of Vaccines and Antivirals during Influenza Pandemics. Geneva; WHO; 2005. [Accessed 5 February 2009]. Available at: http://www.who.int/csr/resources/publications/influenza/11_29_01_A.pdf 12. World Health Organization. WHO strategic action plan for pandemic influenza 2006- 2007. Geneva, WHO, 2006 (WHO/CDS/EPR/GIP/2006.2). [Accessed 25 February 2009]. Available athttp://www.who.int/csr/resources/publications/influenza/StartAcPlanES.pdf 13. World Health Organization. Responding to the avian influenza pandemic threat. Recommended strategic actions. [Accessed 25 February 2009]. Available at: http://www.who.int/csr/resources/publications/influenza/WHO_CDS_CSR_GIP_05_8- EN.pdf 14. World Health Organization. Infection Control Strategies for Specific Procedures in Health-Care Facilities. Epidemic-prone and pandemic-prone acute respiratory diseases. A quick reference guide. WHO, 2008. [Accessed 25 February 2009]. Available at: http://www.paho.org/English/AD/DPC/CD/epi-pan-prone-ards-inf-ctl-quick-guide.pdf 15. Pan American Health Organization. Centers for Disease Control and Prevention (CDC), Atlanta. Generic Protocol for Influenza Surveillance. Washington, D.C. Available at: http://www.paho.org/EnglishAD/DPC/CD/404.asp [TN: Unable to definitively confirm this URL for the English-language document, or to access the document (some current problem with the PAHO site, seemingly).

October 2010 version 33

16. Pan American Health Organization. CD47.R10: Regional Strategy for Maintaining National Vaccination Programs in the Américas. CD47/FR, Rev. 1 (Esp.) 23 January 2007. [Accessed 25 February 2009]. Available at: http://www.paho.org/Spanish/GOV/CD/CD47-fr-s.pdf [TN: As above, unable to verify URL for the English-language document, or to access it.] 17. Pan American Health Organization. Programa AIEPI. World Health Organization. UNICEF. Neumonía. In: Diagnóstico y tratamiento de enfermedades prevalentes graves de la infancia. Washington D.C.:PAHO, 2004. 18. Pan American Health Organization. Effective Management of Vaccination Programs. Module I: Diseases. Washington, D.C.: PAHO, 2006. [TN: This title is taken from PAHO’s description of the publication at http://www.paho.org/English/DD/PUB/Training_Modules.pdf. However, it diverges slightly from the form of the title given in the source document.] 19. Pan American Health Organization. Effective Management of Vaccination Programs. Module II: Vaccines. Washington, D.C.: PAHO, 2006. [TN: See previous note.] 20. Pan American Health Organization. Health Establishments Preparation for Unusual or Unexpected Cases or Clusters of Severe Acute Respiratory Infection (SARI). April 2009. [TN: This is the title I find in an online reference, though the lack of an apostrophe or colon after “Health Establishments” make it potentially suspect. The source doc cites a 2008 version of the publication in Spanish, but April 2009 is the date I found in my online search.] 21. Pan American Health Organization. Clinical management of human infection with pandemic (H1N1) 2009: revised guidance. November 2009. [Accessed 29 November 2010.] Available at: http://www.who.int/csr/resources/publications/swineflu/clinical_management_h1n1.pdf 22. Pan American Health Organization. . Pandemic (H1N1) Regional Update 14 Dec 2009. http://www.reliefweb.int/rw/RWFiles2009.nsf/FilesByRWDocUnidFilename/EGUA- 7YRR4G-full_report.pdf/$File/full_report.pdf [TN: I couldn’t find the English doc on the PAHO site, so cite the URL where I found it. The source doc reference reads: Actualización Semanal Pandemia (H1N1) 2009 (14 de diciembre, 2009--17 h GMT; 12 h EST). [Accessed 16 December 2009]. Available at: http://new.paho.org/hq/index.php?option=com_content&task=blogcategory&id=805&Ite mid=569&lang=es]

October 2010 version 34

23. Pan American Health Organization. 18th meeting of the Technical Advisory Group, Costa Rica, 2009 – Draft Final Report (26 August #2). 24. Webster RG, Peiris M, Chen H, Guan Y. Emerging Infectious Disease online. Vol 12 No 1. January 2006 [cited 28 Feb 2009]. Available at: http://www.cdc.gov/ncidod/EID/vol12no01/pdfs/05-1024.pdf 25. World Health Organization, Influenza Fact Sheet No. 211. Revised March 2003 [cited 1 March 2009]. Available at: http://www.who.int/mediacentre/factsheets/2003/fs211/en/print.html 26. World Health Organization. Resolution WHA 58.5: Strengthening Pandemic Influenza Preparedness and Response. 2005 [cited 1 March 2009]. Available at: http://www.who.int/gb/ebwha/pdf_files/WHA58/WHA58_5-en.pdf 27. World Health Organization. Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO. [Cited 9 November 2008.] Available at: http://www.who.int/csr/disease/avian_influenza/country/cases_table_2008_09_10/en/in dex.html 28. World Health Organization. Recommended laboratory tests to identify avian influenza A virus in specimens from humans. 2005 [cited 28 February 2009]. Available at: http://www.who.int/csr/disease/avian_influenza/guidelines/avian_labtests2.pdf 29. World Health Organization. Situation updates--Avian influenza. 2006 [cited 27 November 2006]. Available at: http://www.who.int/esr/disease/avian_influenza/updates/en/index.html. 30. World Health Organization. Influenza vaccines. WHO position paper. Weekly Epidemiological Record [online series of position papers]. August 2005 [cited 1 March 2009]. No 33(80): 279-287. Available at: http://www.who.int/wer/2005/wer8033.pdf 31. World Organization for Animal Health (OIE). Update on Avian Influenza in Animals (Type H5) 2006 [cited 4 November 2006]. Available at: http://www.oie.int/downld/AVIAN%20INFLUENZA/A_AI-Asia.htm. 32. World Health Organization. Avian Influenza Timeline. [Cited 14 December 2009]. Available at: http://www.who.int/csr/disease/avian_influenza/Timeline090727.pdf 33. World Health Organization. Avian Influenza Timeline. [Cited 2009 Dec 14]. Available at: http://www.who.int/csr/disease/avian_influenza/country/cases_table_2009_12_11/en/pri nt.html

October 2010 version 35

34. World Health Organization. WHO guidelines for investigation of human cases of avian influenza A (H5N1). 2006. Revised 2007 [cited 14 December 2009]. Available at: http://www.who.int/csr/resources/publications/influenza/WHO_CDS_EPR_GIP_2006_4r 1.pdf) 35. Ruvinsky [TN: spelling of the name needs to be corrected in the source doc. No English of this publication found.] R and Balanzat AMC. Neumonías Bacterianas y Virales. In: Infecciones respiratorias en niños. Benguigui Y, Antuñano FJL, Schmunis G, Yunes J, editors. Washington, D.C, Pan American Health Organization. 1997. Pages 215-43. 36. Secretariat of Health of the State of São Paulo. Coordenação dos Institutos de Pesquisa. Instituto Adolfo Lutz. Serviço de Virologia. Laboratório de Vírus Respiratórios. Instruções para colheita, acondicionamento e envio de amostras clínicas. São Paulo, 6 January 2005. [Accessed 28 February 2009]. Available at: ftp://ftp.cve.saude.sp.gov.br/doc_tec/resp/influ_protocolo.pdf 37. Sociedade Brasileira de Pneumologia e Tisiologia. Diretriz para Pneumonias Adquiridas na Comunidade (PAC) em adultos Imunocompetentes. J Bras Pneumol, 2004;30 (Supl 4): S2-S3. 38. Jain S, et al. Hospitalized Patients with 2009 H1N1 Influenza in the United States, April-June 2009. N Engl J Med 2009; 361:1935-44. 39. Zhu FC et al. A Novel Influenza A (H1N1) Vaccine in Various Age Groups. N Engl J Med 2009; 361:2414-23. 40. World Health Organization. Pandemic influenza A (H1N1) 2009 virus vaccine – conclusions and recommendations from the October 2009 meeting of the immunization Strategic Advisory Group of Experts. Weekly Epidemiological Record No. 49, 2009, 84, 505-516. [Cited 22 February 2010.] Available at: http://www.who.int/wer

October 2010 version 36

ANNEX I - Collecting, Storing and Transporting Specimens of Respiratory Secretions for Virus Identification

Types of specimens • In cases of ILI or SARI, nasopharyngeal and oropharyngeal swabs are collected from adults and children five and older • For children under five, a nasopharyngeal aspirate is recommended. • An aspirate is also recommended when it is not possible to collect a swab

Techniques for collecting specimens • Nasopharngeal swab o or fiber swabs should be used; do not use calcium alginate or swabs with wooden stems o Insert a dry swab in the nostril and move it inward to the nasopharynx o Hold it there for a few seconds o Slowly remove the swab while rotating gently. o Put the swab in the tube containing the transport media Figure 1 Collecting a nasal swab

October 2010 version 37

• Oropharyngeal swab o Ask the patient to open his or her mouth o Lower the tongue with the depressor o Use the swab to take a specimen from the posterior o Avoid contact with the o Place the swab in the transport media

NOTE: If the medium has been prepared in the laboratory, the nasopharyngeal and oropharyngeal swabs can be put in the same transport media

• Nasopharyngeal aspirate o Review the expiration date of the transport media, aspiration tube, and vacuum pump o Break open the envelope with the aspiration kit and connect the smaller-diameter end of the tube to a sterile probe o Use the probe to measure the distance from the nose to the base of the ear; half of this distance equals the distance between the patient’s nose and oropharynx o Connect the larger-diameter end of the tube to the vacuum pump o Insert the probe in the patient’s nostril o Withdraw the probe, rotating gently o Repeat the procedure in the other nostril o Draw a volume of approximately 8-10 ml of cold tampon solution (pH 7.2) through the probe to remove all the secretion o Change the cover of the collector tube

Source: Johns Hopkins Hospital Epidemiology and Infectious Control and Nursing Education Department

October 2010 version 38

NOTE: For all specimens, according to the algorithm, send specimens to the laboratory immediately, along with the form designed to accompany specimens; specimens should be refrigerated until arrival in the laboratory and should never be frozen

Preserving and transporting specimens • If using a commercial media, place the swab in the transport tube and press the bottom of the tube or press the pad at the bottom to release the media; if the media is prepared in the laboratory, cut the stem of the swab so that only the part adhering to the swab remains and close the tube with the cap • Swabs must always be kept moist while being transported • The tube with the media and the swab should be kept refrigerated at 4-8oC in a thermos for holding specimens • Transfer the specimens to the laboratory that is to process them as soon as possible (preferably within 24 hours, but within 48 hours at most) • Follow the recommendations of the United Nations Committee of Experts on the Transportation of Dangerous Goods

October 2010 version 39

ANNEX II–Evaluation and Analysis of Surveillance Data

Nº Indicator Structure Observations Value SURVEILLANCE INDICATORS Number of EWs with timely Timeliness of notification of Timely is considered as the reporting of denominators on the pre‐ 1 notification of denominators/Total EWs notified specified day each week denominators x 100

Median interval in the days Timeliness of between the hospitalization date 2 reporting of cases and the notification date

Total number of completely investigated and closed SARI Investigation 3 cases/ Total of cases reported coverage with a sample x 100

LABORATORY INDICATORS Number of SARI cases with Coverage of SARI collected sample/Number of SARI Criteria for sample collection are those that fall within the interval of 4 sampled cases cases with criteria for sample 7 days since the onset date of the fever collection

Number of SARI cases in ICU with Coverage of sampled collected sample/Number of SARI 5 SARI cases in ICU cases in ICU x 100

Coverage of Number of SARI death cases with 6 sampled SARI deaths collected samples/Number of cases SARI deaths X 100

October 2010 version 51

Nº Indicator Structure Observations Value Median of the interval in the days between date of 7 Timing of sampling hospitalization and date of sampling Median of the interval in the Timing of receipt of days between date of sampling In case the receipt date is not available calculate this indicator with 8 the sample and date of receipt of the the shipping date sample Number of quality samples Quality of the Quality is defined as, the samples were correctly sampled, conserved 9 receipt/ Total of samples sample and transported until the l arrival in the laboratory receipt x 100 Number of processed samples/ 10 Processing coverage Total of samples receipt The sample was collected from a person meeting the case definition correctly x 100 Median of the interval between Processing 11 receipt date and beginning of opportunity the processing Median of the interval between Timely of delivery of 12 the date of reception and results delivery of result

October 2010 version 52

ANNEX III – Infection Control Principles of Infection Control The concept of the chain of infection, with its’ links stretching from the infectious agent to the susceptible host through a transmission mechanism, helps to explain how infection occurs and facilitates understanding of infection control mechanisms, which operate by breaking a link in the chain

Pathogen

Susceptible Reservoir Host

Portal of Portal of Entry Exit

Mode of Transmission

Types of transmission The mode of transmission varies from one to another and some can be transmitted by more than one route. The three most important modes of transmission are: contact, droplet, or airborne. • Transmission by contact

October 2010 version 56

Microorganisms can be transmitted through direct or indirect contact with the patient or his/her contaminated body fluids. Direct transmission occurs when are transferred from person to person without an intermediate contaminated object.. Indirect transmission occurs when an infectious agent is transferred through an intermediate contaminated object. Contact precautions should be observed with various pathogens, which include Varicella and Clostridium difficile. With certain pathogens, contact precautions will be employed in addition to another precaution (e.g. airborne or droplet).

• Droplet transmission Droplet transmission involves contact between droplets with particles containing microorganisms from a person who is clinically ill or is a carrier of a microorganism, and the nasal or oral conjunctiva or mucous membranes of a susceptible person. Droplets are most often generated when an infected person coughs, sneezes, or converses. Transmission by droplet requires close contact between source and host, because the droplets do not remain suspended for long and thus usually only travel short distances through the air (~one meter). The respiratory pathogens transmitted through droplets include adenovirus, human influenza virus, SARS and avian influenza A (H5N1).

Droplet transmission is the most important route of transmission for the influenza virus

• Airborne transmission

Pathogens transmitted via this route are also transmitted via mucosal membrane contact with aerosolized droplets of an infectious person. The difference from droplet precautions is that the aerosolized particles are smaller, can travel larger distances, and remain in the air longer. The management of this type of transmission depends on special air management and ventilation systems (e.g. rooms with negative pressure). Examples of pathogens transmitted via this route are M.tuberculosis and the measles virus.

Routine precautions for infection control Standard precautions

October 2010 version 57

October 2010 version 58

Hand October 2010 version 59

Hand hygiene is one of the most important ways of preventing and controlling the spread of disease in health care facilities and is a principal component of standard precautions. Below, we see a diagram depicting the five opportunities for hand hygiene during a clinical encounter in the hospital setting and also in the following figure, we see the appropriate technique for hand-washing with soap and water and hand-rubbing with alcohol.

October 2010 version 60

October 2010 version 61

ANNEX IV – Data Collection Forms

Top View